Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(stringr)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name
## [1] "cd8"
graph_weight
## [1] "10.0"

Check enrichment of gene sets

Read in gene info and gene set assignments

file_tag = sprintf("%s_BL_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, USE.NAMES=FALSE, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    3.00   23.00   24.00   23.73   25.00   27.00
length(n_genes)
## [1] 40
sort(n_genes)
##  [1]  3 20 21 21 22 22 22 23 23 23 23 24 24 24 24 24 24 24 24 24 24 25 25 25 25
## [26] 25 25 25 25 25 25 25 26 26 26 26 26 27 27 27

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}
## [1] "QARS"
## [1] "EPRS1" "QARS1"
## [1] "SEPT2"
## [1] "SEPTIN6" "SEPTIN2"
table(is.na(a2s))
## 
## FALSE  TRUE 
##  1607    42
table(a2s == assayed_genes, useNA = 'ifany')
## 
## FALSE  TRUE  <NA> 
##    42  1565    42
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]
##     sym_in_data sym_limma
##  1:    C10orf91 LINC02870
##  2:    C12orf10      MYG1
##  3:    C12orf45  NOPCHAP1
##  4:     C6orf48    SNHG32
##  5:     C6orf99 LINC02901
##  6:    CXorf40A     EOLA1
##  7:     CXorf57      RADX
##  8:     FAM102A     EEIG1
##  9:     FAM173A    ANTKMT
## 10:     FAM213B    PRXL2B
## 11:       H2AFX      H2AX
## 12:   HIST1H2AG    H2AC11
## 13:   HIST1H2BK    H2BC12
## 14:   HIST1H2BN    H2BC15
## 15:    HIST1H3A      H3C1
## 16:    HIST1H3H     H3C10
## 17:    HIST1H4C      H4C3
## 18:   HIST2H2BF    H2BC18
## 19:    KIAA0391     PRORP
## 20:        QARS     EPRS1
## 21:       SEPT6   SEPTIN6
## 22:       ARNTL     BMAL1
## 23:    C12orf65     MTRFR
## 24:    C16orf72   HAPSTR1
## 25:      CCDC84   CENATAC
## 26:      DOPEY2     DOP1B
## 27:     FAM126B     HYCC2
## 28:    FAM160B1    FHIP2A
## 29:        H1FX     H1-10
## 30:       H2AFJ      H2AJ
## 31:       HEXDC      HEXD
## 32:    HIST1H1C      H1-2
## 33:    HIST1H1D      H1-3
## 34:    HIST1H1E      H1-4
## 35:    KIAA1109     BLTP1
## 36:    KIAA1551     RESF1
## 37:        MKL1     MRTFA
## 38:       NARFL     CIAO3
## 39:       SEPT2   SEPTIN6
## 40:      TARSL2     TARS3
## 41:      TMEM8A     PGAP6
## 42:       WDR60   DYNC2I1
##     sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")), 
                gene_symbol := sym_limma]

dim(gene_info)
## [1] 1649    3
gene_info[1:5,]
##    sym_in_data sym_limma gene_symbol
## 1:      ABLIM1    ABLIM1      ABLIM1
## 2:  AC004687.1      <NA>  AC004687.1
## 3:  AC004854.2      <NA>  AC004854.2
## 4:  AC007384.1      <NA>  AC007384.1
## 5:  AC007952.4      <NA>  AC007952.4
t1 = table(gene_info$gene_symbol)
table(t1)
## t1
##    1    2 
## 1647    1
gene_info[gene_symbol %in% names(t1)[t1 == 2],]
##    sym_in_data sym_limma gene_symbol
## 1:       SEPT6   SEPTIN6     SEPTIN6
## 2:       SEPT2   SEPTIN6     SEPTIN6
gene_info[sym_in_data == "HIST1H2BC", gene_symbol:="H2BC4"]
gene_info[sym_in_data == "HIST1H2BG", gene_symbol:="H2BC8"]
gene_info[sym_in_data == "SEPT6", gene_symbol:="SEPTIN6"]
gene_info[sym_in_data == "SEPT2", gene_symbol:="SEPTIN2"]

Read in cell type-specific expression data

Cell type specific gene expression were downloaded from protein atlas.

ct = fread("../Annotation/rna_single_cell_type.tsv.gz")
dim(ct)
## [1] 1587110       4
ct[1:5,]
##               Gene Gene name             Cell type  nTPM
## 1: ENSG00000000003    TSPAN6            Adipocytes 149.5
## 2: ENSG00000000003    TSPAN6 Alveolar cells type 1   6.1
## 3: ENSG00000000003    TSPAN6 Alveolar cells type 2  10.5
## 4: ENSG00000000003    TSPAN6            Astrocytes  13.9
## 5: ENSG00000000003    TSPAN6               B-cells   1.5
length(unique(ct$`Cell type`))
## [1] 79
table(ct$`Cell type`)
## 
##                      Adipocytes           Alveolar cells type 1 
##                           20090                           20090 
##           Alveolar cells type 2                      Astrocytes 
##                           20090                           20090 
##                         B-cells             Basal keratinocytes 
##                           20090                           20090 
##           Basal prostatic cells         Basal respiratory cells 
##                           20090                           20090 
## Basal squamous epithelial cells                   Bipolar cells 
##                           20090                           20090 
##          Breast glandular cells      Breast myoepithelial cells 
##                           20090                           20090 
##                  Cardiomyocytes                  Cholangiocytes 
##                           20090                           20090 
##                      Club cells           Collecting duct cells 
##                           20090                           20090 
##        Cone photoreceptor cells                Cytotrophoblasts 
##                           20090                           20090 
##                 dendritic cells              Distal enterocytes 
##                           20090                           20090 
##            Distal tubular cells                    Ductal cells 
##                           20090                           20090 
##                Early spermatids      Endometrial ciliated cells 
##                           20090                           20090 
##       Endometrial stromal cells               Endothelial cells 
##                           20090                           20090 
##           Enteroendocrine cells                 Erythroid cells 
##                           20090                           20090 
##              Excitatory neurons        Exocrine glandular cells 
##                           20090                           20090 
##       Extravillous trophoblasts                     Fibroblasts 
##                           20090                           20090 
##   Gastric mucus-secreting cells     Glandular and luminal cells 
##                           20090                           20090 
##                    granulocytes                 Granulosa cells 
##                           20090                           20090 
##                     Hepatocytes                  Hofbauer cells 
##                           20090                           20090 
##                Horizontal cells              Inhibitory neurons 
##                           20090                           20090 
##         Intestinal goblet cells                       Ionocytes 
##                           20090                           20090 
##                   Kupffer cells                Langerhans cells 
##                           20090                           20090 
##                 Late spermatids                    Leydig cells 
##                           20090                           20090 
##                     Macrophages                     Melanocytes 
##                           20090                           20090 
##                Microglial cells                       monocytes 
##                           20090                           20090 
##           Mucus glandular cells               Muller glia cells 
##                           20090                           20090 
##                        NK-cells Oligodendrocyte precursor cells 
##                           20090                           20090 
##                Oligodendrocytes      Pancreatic endocrine cells 
##                           20090                           20090 
##                    Paneth cells               Peritubular cells 
##                           20090                           20090 
##                    Plasma cells       Prostatic glandular cells 
##                           20090                           20090 
##            Proximal enterocytes          Proximal tubular cells 
##                           20090                           20090 
##      Respiratory ciliated cells         Rod photoreceptor cells 
##                           20090                           20090 
##             Salivary duct cells                   Schwann cells 
##                           20090                           20090 
##          Serous glandular cells                   Sertoli cells 
##                           20090                           20090 
##               Skeletal myocytes             Smooth muscle cells 
##                           20090                           20090 
##                   Spermatocytes                   Spermatogonia 
##                           20090                           20090 
##       Squamous epithelial cells        Suprabasal keratinocytes 
##                           20090                           20090 
##            Syncytiotrophoblasts                         T-cells 
##                           20090                           20090 
##                     Theca cells         Thymic epithelial cells 
##                           20090                           20090 
##          Undifferentiated cells 
##                           20090
ct_immune = fread("../Annotation/rna_immune_cell_monaco.tsv.gz")
dim(ct_immune)
## [1] 602700      5
ct_immune[1:5,]
##               Gene Gene name                Immune cell TPM pTPM
## 1: ENSG00000000003    TSPAN6                   basophil  NA  1.2
## 2: ENSG00000000003    TSPAN6  Central memory CD8 T-cell  NA  1.7
## 3: ENSG00000000003    TSPAN6         classical monocyte  NA  0.2
## 4: ENSG00000000003    TSPAN6 Effector memory CD8 T-cell  NA  0.7
## 5: ENSG00000000003    TSPAN6    Exhausted memory B-cell  NA  0.7
summary(ct_immune$TPM)
##    Mode    NA's 
## logical  602700
summary(ct_immune$pTPM)
##     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
##     0.00     0.00     3.10    49.74    27.20 96572.50
summary(ct_immune$pTPM[ct_immune$pTPM > 0])
##     Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
##     0.10     1.70    11.60    67.96    42.80 96572.50
length(unique(ct_immune$`Immune cell`))
## [1] 30
table(ct_immune$`Immune cell`)
## 
##                            basophil           Central memory CD8 T-cell 
##                               20090                               20090 
##                  classical monocyte          Effector memory CD8 T-cell 
##                               20090                               20090 
##             Exhausted memory B-cell               intermediate monocyte 
##                               20090                               20090 
##                         MAIT T-cell               Memory CD4 T-cell TFH 
##                               20090                               20090 
##               Memory CD4 T-cell Th1          Memory CD4 T-cell Th1/Th17 
##                               20090                               20090 
##              Memory CD4 T-cell Th17               Memory CD4 T-cell Th2 
##                               20090                               20090 
##                          myeloid DC                        naive B-cell 
##                               20090                               20090 
##                    naive CD4 T-cell                    naive CD8 T-cell 
##                               20090                               20090 
##                          neutrophil                             NK-cell 
##                               20090                               20090 
##              non-classical monocyte          Non-switched memory B-cell 
##                               20090                               20090 
##                       Non-Vd2 gdTCR                         Plasmablast 
##                               20090                               20090 
##                     plasmacytoid DC                     Progenitor cell 
##                               20090                               20090 
##              Switched memory B-cell                               T-reg 
##                               20090                               20090 
## Terminal effector memory CD4 T-cell Terminal effector memory CD8 T-cell 
##                               20090                               20090 
##                          total PBMC                           Vd2 gdTCR 
##                               20090                               20090
lineage = fread("../Annotation/rna_immune_cell_monaco_cell_types.tsv")
dim(lineage)
## [1] 30  2
lineage[1:2,]
##     Cell_type      Lineage
## 1:   Basophil Granulocytes
## 2: Neutrophil Granulocytes

Check gene expression for each gene set

dim(gene_info)
## [1] 1649    3
for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]

  n_genes = sum(genes %in% ct_immune$`Gene name`)
  print(sprintf("found %d genes.", n_genes))

  if(n_genes == 0) { next }

  df = ct_immune[`Gene name` %in% genes,]
  dim(df)
  df[1:2,]
  
  stopifnot(all(str_to_lower(df$`Immune cell`) %in% 
                  str_to_lower(lineage$Cell_type)))
  
  mat1 = match(str_to_lower(df$`Immune cell`), 
               str_to_lower(lineage$Cell_type))
  
  df = cbind(df, lineage[mat1,])
  df[1:2,]
  
  df$Cell_type = factor(df$Cell_type, levels = lineage$Cell_type)
  df = df[df$Lineage != "Total PBMC",]
  df$Lineage   = factor(df$Lineage, 
                        levels = setdiff(lineage$Lineage, "Total PBMC"))
  
  p1 = ggplot(df, aes(x=Cell_type, y=log10(pTPM + 0.1), fill=Lineage)) + 
    geom_boxplot() + xlab("Cell type") + ggtitle(set_k) + 
    theme(axis.text.x = element_text(angle = 45, hjust = 1)) + 
    scale_fill_brewer(palette="RdBu")

  print(p1)
}
## [1] 1
##  [1] "AC008555.5" "AC012645.3" "AC044849.1" "AC087623.3" "AC119396.1"
##  [6] "AC245297.3" "ARRDC2"     "CCL4L2"     "CLDND1"     "CRLF3"     
## [11] "EOMES"      "HIKESHI"    "INTS6L"     "LINC00649"  "PITPNC1"   
## [16] "TRAV8-3"    "TRGV7"      "TRGV8"      "ADGRG1"     "ARHGAP30"  
## [21] "CYTOR"      "FCRL6"      "NECAP1"     "TTC38"      "XCL2"      
## [1] "found 16 genes."

## [1] 2
##  [1] "AK5"        "CHRM3-AS2"  "COQ8A"      "IGLV1-44"   "LINC00402" 
##  [6] "LST1"       "MATR3-1"    "PDCD4-AS1"  "RETREG1"    "TC2N"      
## [11] "TRAV14DV4"  "TRAV8-2"    "TRBV28"     "TRBV9"      "CLEC16A"   
## [16] "DOCK10"     "HIPK1"      "HRH2"       "IFI27"      "NUTM2B-AS1"
## [21] "PIK3CD"     "POLR2J3-1"  "PPP4R3B"    "PUM3"       "S100A12"   
## [26] "TUT4"      
## [1] "found 20 genes."

## [1] 3
##  [1] "NUAK2"    "TBCCD1"   "ABCA7"    "ARHGAP10" "BTBD9"    "DMTF1"   
##  [7] "ERBIN"    "FAM126B"  "FAM78A"   "GK5"      "HECA"     "IRF9"    
## [13] "MCTP2"    "MYBL1"    "MYO1F"    "NFATC3"   "NRDC"     "OGA"     
## [19] "PARP15"   "PATL2"    "PIK3R5"   "RASGRP1"  "RNF125"   "SIDT1"   
## [25] "TUT7"     "XIST"    
## [1] "found 24 genes."

## [1] 4
##  [1] "CCR7"       "FXYD7"      "LTB"        "SLC2A3"     "AC016831.7"
##  [6] "ARHGAP45"   "ARHGEF9"    "ATAD2B"     "BMT2"       "ETFDH"     
## [11] "FAM133B"    "GABPB2"     "GPHN"       "HPS4"       "KAT6B"     
## [16] "LINC02446"  "MARF1"      "OXNAD1"     "PCED1B"     "PNPLA8"    
## [21] "PSMA3-AS1"  "RIPOR2"     "SEC14L1"    "THAP5"      "TMEM131L"  
## [26] "ZNF83"     
## [1] "found 23 genes."

## [1] 6
##  [1] "HLA-DMB"  "KLRB1"    "KLRC3"    "KLRK1"    "MAN2B1"   "OXA1L"   
##  [7] "TFB2M"    "TIGIT"    "CMKLR1"   "CSNK1G2"  "GALNT10"  "GDPD5"   
## [13] "ITGAM"    "KIR2DL3"  "RAPGEF1"  "SLC20A1"  "SLC38A10" "TIMP1"   
## [19] "TMEM127"  "TMEM181"  "TMEM8A"   "TTC17"   
## [1] "found 22 genes."

## [1] 7
##  [1] "CCNB1IP1" "ADGRE5"   "ARL4C"    "CARD11"   "CARD16"   "CD52"    
##  [7] "CTSW"     "CX3CR1"   "DDX60L"   "IFITM2"   "ITM2A"    "KDM3B"   
## [13] "KIAA1551" "LAG3"     "LY6E"     "MT2A"     "MYO1G"    "RALGAPB" 
## [19] "S100A11"  "TRAC"     "TRAV12-3" "TRAV17"   "TRAV9-2"  "TRBV11-2"
## [25] "TRGC2"    "ZNF683"  
## [1] "found 24 genes."

## [1] 8
##  [1] "AIF1"    "CHMP1B"  "NSUN6"   "CASP10"  "CAST"    "CCDC88C" "CD46"   
##  [8] "CELF2"   "CFLAR"   "DDHD1"   "DENND6A" "ITK"     "KCNAB2"  "KDM5A"  
## [15] "KLF3"    "LRBA"    "MTMR6"   "NCKAP1L" "PCYT1A"  "PRKCH"   "RASA3"  
## [22] "RIC3"    "SPG11"   "WDR7"   
## [1] "found 24 genes."

## [1] 9
##  [1] "ID2"     "ISCA1"   "MAP3K2"  "MSC"     "NDE1"    "SPECC1"  "ABHD17A"
##  [8] "BHLHE40" "DOCK11"  "EFHD2"   "FRYL"    "GSE1"    "LENG8"   "MACF1"  
## [15] "MAP3K3"  "PHF3"    "PLEKHG3" "POLH"    "PRR5L"   "PTPN23"  "SSH1"   
## [22] "STK38"   "WAC"     "ZFYVE16"
## [1] "found 24 genes."

## [1] 10
##  [1] "CD27"         "CPNE1"        "CREBL2"       "CYB561A3"     "EPB41L4A-AS1"
##  [6] "FCER1G"       "IER3"         "ITGAE"        "KIR3DL2"      "LRRC23"      
## [11] "NCR1"         "NR4A3"        "NT5DC1"       "SDR42E2"      "SLC38A1"     
## [16] "TMEM107"      "TMEM204"      "TMEM42"       "TSPYL4"       "UIMC1"       
## [21] "ZFAND1"       "PARP4"        "TEP1"         "TRIM38"      
## [1] "found 23 genes."

## [1] 11
##  [1] "GLA"     "MAT2B"   "ARHGEF3" "ARID5B"  "BROX"    "CAPNS1"  "GCN1"   
##  [8] "GPRIN3"  "IL2RG"   "INO80D"  "KLF2"    "KLF6"    "NCOA7"   "NLRC5"  
## [15] "PLA2G6"  "PLAC8"   "SENP7"   "SLFN12L" "STK17B"  "TOB1"    "USP16"  
## [22] "XAF1"    "ZBP1"    "ZBTB20"  "ZDHHC20"
## [1] "found 25 genes."

## [1] 12
##  [1] "THAP9-AS1"   "AKNA"        "AP005482.1"  "CEMIP2"      "DIAPH2"     
##  [6] "GPR174"      "LINC02384"   "MIAT"        "MX2"         "NBEAL2"     
## [11] "OAS2"        "ODF3B"       "PCSK7"       "SAMD9L"      "TBC1D14"    
## [16] "THUMPD3-AS1" "TRANK1"      "TRAPPC11"    "TRAPPC8"     "TRAV19"     
## [21] "TRAV27"      "TRAV4"       "TRBV2"       "TRDV1"       "TRGV10"     
## [26] "TRGV4"       "TSPAN32"    
## [1] "found 22 genes."

## [1] 13
##  [1] "AC083798.2" "AL121944.1" "ARMH1"      "ATP2B1-AS1" "BBS9"      
##  [6] "FAM213B"    "IGKV3-20"   "INPP4B"     "LRRN3"      "NPIPB4"    
## [11] "NUP58"      "PRAG1"      "RAB33B"     "SLC27A5"    "TNFRSF25"  
## [16] "TRABD2A"    "TRAV12-2"   "TRAV5"      "TRAV8-4"    "TRBV3-1"   
## [21] "TRBV6-1"    "TRBV6-2"    "ZNF749"     "ZNF862"     "MTERF2"    
## [26] "RUFY2"      "SLCO3A1"   
## [1] "found 24 genes."

## [1] 14
##  [1] "AC007384.1" "AC020911.2" "AC025171.3" "AC083880.1" "AC091271.1"
##  [6] "AC103591.3" "AF213884.3" "AL139246.5" "AL357060.1" "AL451085.1"
## [11] "AL627171.1" "ASL"        "C6orf99"    "HELQ"       "HIPK1-AS1" 
## [16] "IFRD1"      "KCNQ1OT1"   "LINC01465"  "MZF1-AS1"   "NT5C3B"    
## [21] "OSER1-DT"   "PGGHG"      "RGS1"       "TRAV3"      "TRBV7-9"   
## [26] "C16orf72"   "HIVEP3"    
## [1] "found 9 genes."

## [1] 15
##  [1] "ACTR1B"   "C12orf10" "EIF1"     "EIF2S3"   "EIF3E"    "EIF3G"   
##  [7] "EIF3K"    "EIF3L"    "EIF4A2"   "PAIP2"    "PHLDA1"   "RACK1"   
## [13] "ATAD2"    "DDX60"    "EIF3A"    "EIF4G1"   "EIF4G3"   "LRRFIP1" 
## [19] "MSI2"     "PRRC2C"   "SECISBP2"
## [1] "found 21 genes."

## [1] 16
##  [1] "AC004687.1" "AC087239.1" "AL118516.1" "AL138963.3" "ANXA2R"    
##  [6] "ATP5F1A"    "BTG2"       "CCNI"       "CMC1"       "FCMR"      
## [11] "GCSAM"      "GTF3A"      "ICAM3"      "KLRF1"      "MFNG"      
## [16] "NBPF14"     "NOP53"      "PPP1R15B"   "PRR7"       "RTRAF"     
## [21] "SNHG15"     "SNHG9"      "TRG-AS1"    "WDR86"      "WSB1"      
## [26] "ZNF276"    
## [1] "found 19 genes."

## [1] 17
##  [1] "ARL4A"   "IL6R"    "RGCC"    "TXK"     "UBL7"    "ZC3H12A" "ZNF10"  
##  [8] "CLUH"    "COX19"   "ELMO1"   "ETV6"    "GON4L"   "LONP2"   "NAA25"  
## [15] "NFKBIZ"  "PARP14"  "PARP9"   "PDE4B"   "PHF14"   "PIGF"    "SETD2"  
## [22] "USP34"   "WDR37"   "ZNF557" 
## [1] "found 24 genes."

## [1] 18
##  [1] "AKTIP"     "GLS"       "HIST1H2BK" "HIST1H2BN" "IL16"      "NCF1"     
##  [7] "PPA1"      "SSR2"      "TBC1D17"   "BDP1"      "CPT1A"     "CYBA"     
## [13] "DHX29"     "FGR"       "NEMF"      "NNT"       "PKD1"      "PPP1R12C" 
## [19] "PTMS"      "UPF2"     
## [1] "found 20 genes."

## [1] 19
##  [1] "ASAH1"    "ATP5MG"   "CD7"      "GATA3"    "GRAMD1A"  "MZT2A"   
##  [7] "MZT2B"    "PNRC1"    "PPP1R15A" "PTGER4"   "VAMP7"    "CD99"    
## [13] "DNAJB14"  "KLHDC4"   "NUP210"   "PTPN4"    "PTPN7"    "RORA"    
## [19] "ST6GAL1"  "TBX21"    "TUBGCP6"  "ZFAND3"  
## [1] "found 22 genes."

## [1] 20
##  [1] "ARHGAP9"  "C12orf45" "CXXC5"    "EI24"     "GIMAP1"   "GPR183"  
##  [7] "GSTM1"    "GSTM4"    "LCP2"     "LETMD1"   "PCMTD2"   "PDE7A"   
## [13] "RTN3"     "SESN2"    "TRAT1"    "ARAP2"    "FAM169A"  "LRRC8A"  
## [19] "MCOLN2"   "MICAL2"   "SZT2"     "VPS13A"   "VPS13D"  
## [1] "found 22 genes."

## [1] 21
##  [1] "CAMK4"    "CMTM7"    "EPHX2"    "EPS8"     "FAM102A"  "HIBADH"  
##  [7] "LDLRAP1"  "NOSIP"    "RCAN3"    "SELL"     "STMN3"    "TCEA3"   
## [13] "TCF7"     "TESPA1"   "TRAV21"   "ZNF575"   "GPANK1"   "HERC3"   
## [19] "HERC6"    "ITPR2"    "MAPK8IP3" "SCRN3"    "SOS1"     "VCAN"    
## [25] "ZNF493"  
## [1] "found 24 genes."

## [1] 22
##  [1] "AMD1"     "C12orf57" "CD84"     "DTHD1"    "FAM118A"  "GLTP"    
##  [7] "GZMK"     "KLRG1"    "NOCT"     "PIK3IP1"  "RCSD1"    "RGL4"    
## [13] "RSRP1"    "SH2D1A"   "SLC38A2"  "STK17A"   "TOX"      "TRBC1"   
## [19] "TRGV5"    "WARS2"    "CCDC112"  "ERAP2"    "SLK"      "VPS13B"  
## [25] "YPEL1"   
## [1] "found 25 genes."

## [1] 23
##  [1] "ALOX5AP" "APMAP"   "HDHD3"   "LAPTM5"  "LBH"     "LIME1"   "MATK"   
##  [8] "PTPRCAP" "PTRHD1"  "RHOC"    "THEM4"   "TMEM134" "CBX7"    "CST7"   
## [15] "FGFBP2"  "GZMA"    "GZMB"    "NKG7"    "PHC3"    "PLEK"    "SPON2"  
## [22] "SRGN"    "UBE4A"   "UCP2"   
## [1] "found 24 genes."

## [1] 24
##  [1] "NT5E"    "SNRPN"   "ZEB1"    "AFF1"    "AFF4"    "ARID1A"  "ARID1B" 
##  [8] "BAZ2A"   "CHD1"    "CRNKL1"  "DGKD"    "NKTR"    "PIP4K2B" "PNN"    
## [15] "PPIG"    "RNF157"  "RNMT"    "RNPC3"   "SCAF8"   "SMG1"    "USP42"  
## [22] "WDR60"  
## [1] "found 22 genes."

## [1] 25
##  [1] "BTG1"     "FOXP1"    "KLHDC2"   "PPP1R10"  "PRPF38B"  "SAT1"    
##  [7] "SATB1"    "ZBTB10"   "ARHGAP4"  "ASH1L"    "FAM160B1" "HERC1"   
## [13] "MALAT1"   "MORC3"    "NEAT1"    "RUNX3"    "SLTM"     "TCF25"   
## [19] "TFDP2"    "TTF2"     "ZC3H7B"   "ZEB2"     "ZNF335"  
## [1] "found 20 genes."

## [1] 26
##  [1] "AC004854.2"  "AC015982.1"  "AC016405.3"  "AC027644.3"  "AOAH"       
##  [6] "ARF4-AS1"    "BX284668.6"  "CRTAM"       "CSKMT"       "CXorf40A"   
## [11] "IER5"        "ILF3-DT"     "KLF10"       "KMT2E-AS1"   "MAPRE2"     
## [16] "MTRNR2L8"    "PAPSS1"      "SLC4A4"      "TRAV38-2DV8" "TRBV6-5"    
## [21] "TRBV7-2"     "TRGV9"       "Z93241.1"    "GALNT3"      "RLF"        
## [1] "found 16 genes."

## [1] 27
##  [1] "HMGCS1"   "RELT"     "TPRKB"    "CAPN15"   "DNAJC13"  "EPSTI1"  
##  [7] "GPATCH2L" "HSH2D"    "IFI44"    "IFI44L"   "IGHA1"    "IGKC"    
## [13] "MBD5"     "MX1"      "PHF11"    "PPM1K"    "PRKX"     "PTPRJ"   
## [19] "RNF213"   "S100A8"   "SPOCK2"   "STK10"    "TTC14"   
## [1] "found 23 genes."

## [1] 28
##  [1] "LPXN"    "C2CD3"   "CEP164"  "CEP350"  "CTDSPL2" "DENND4C" "ENTPD4" 
##  [8] "GIGYF1"  "HELZ2"   "HIPK3"   "IFIT2"   "IFIT3"   "KIF13B"  "LIMD1"  
## [15] "MAN2C1"  "N4BP1"   "PHACTR4" "PSTPIP2" "REXO1"   "RIF1"    "SMCHD1" 
## [22] "ZCCHC2"  "ZNF292"  "ZNF800" 
## [1] "found 24 genes."

## [1] 29
##  [1] "CST3"     "CYB5D2"   "GALNT11"  "INTS8"    "PDE3B"    "SAE1"    
##  [7] "ADAM10"   "AHCTF1"   "ASCL2"    "CHST12"   "CTSC"     "DOPEY2"  
## [13] "FAR1"     "GALNT2"   "HLA-DQA1" "HLA-DRB1" "KLRD1"    "LILRB1"  
## [19] "LPCAT1"   "MPPE1"    "MYO9B"    "PDE12"    "PNPLA6"   "PRF1"    
## [1] "found 24 genes."

## [1] 30
##  [1] "ABCC10"     "AC092683.1" "AC116407.2" "ADCY7"      "AP3M2"     
##  [6] "CCDC84"     "CREBZF"     "ELMOD3"     "GPR132"     "GRK2"      
## [11] "IGKV3-15"   "LINC02256"  "MIGA1"      "PCNX1"      "RUBCN"     
## [16] "SLF2"       "SPATA13"    "TENT5C"     "TRBV4-2"    "TRBV7-6"   
## [21] "TTTY15"     "UTY"        "Z93930.2"   "ZNF652"     "ZNF808"    
## [1] "found 20 genes."

## [1] 31
##  [1] "COMMD6"   "COTL1"    "RPL41"    "TOMM7"    "TPGS2"    "TRAF3IP2"
##  [7] "YPEL3"    "ARHGAP35" "B2M"      "CD8A"     "CD8B"     "FNDC3B"  
## [13] "GCA"      "HEXDC"    "KIAA0232" "LSS"      "MKL1"     "OAS3"    
## [19] "POLG"     "PRSS23"   "SBK1"     "TAF1D"    "TMSB10"   "TMSB4X"  
## [1] "found 24 genes."

## [1] 32
##  [1] "CD28"     "TLE4"     "ARAP1"    "C5orf24"  "CCL4"     "CES1"    
##  [7] "CROCC"    "ETNK1"    "GNLY"     "GNPTAB"   "GPR141"   "INPP5D"  
## [13] "KIAA2026" "MKLN1"    "NARFL"    "PDZD4"    "PEX1"     "PEX26"   
## [19] "SEMA4D"   "ST8SIA4"  "SUSD1"    "SYNE1"    "UBR2"     "WDTC1"   
## [25] "YPEL5"   
## [1] "found 25 genes."

## [1] 33
##  [1] "FCRL3"    "ITGB1BP1" "ANKRD12"  "APOL6"    "BTN3A1"   "CCNH"    
##  [7] "CD38"     "EML4"     "ERICH1"   "FAM13B"   "ITGAL"    "PREX1"   
## [13] "PYROXD1"  "RHOH"     "SLA2"     "SLC35F5"  "SLFN5"    "STAT4"   
## [19] "SYNRG"    "TAOK1"    "TAOK3"    "TIPARP"   "TRBC2"    "UNC13D"  
## [25] "ZAP70"   
## [1] "found 25 genes."

## [1] 34
##  [1] "AC025164.1" "AL135791.1" "ALKBH7"     "BEX4"       "BNIP3L"    
##  [6] "C6orf48"    "CD40LG"     "COA1"       "HIST1H3H"   "JAML"      
## [11] "LINC02273"  "MCUB"       "MYLIP"      "NR1D1"      "SESN1"     
## [16] "SNHG12"     "TMIGD2"     "TRAV1-2"    "TRAV13-1"   "TRBV20-1"  
## [21] "CISH"       "CRYBG1"     "R3HCC1L"    "RFWD3"      "SETX"      
## [1] "found 20 genes."

## [1] 35
##  [1] "AC007952.4" "AC245014.3" "CITED2"     "COQ7"       "CSRNP1"    
##  [6] "DYRK4"      "EFCAB2"     "FAM173A"    "GADD45B"    "GLRX5"     
## [11] "IER2"       "KCTD7"      "MPST"       "MZF1"       "NELL2"     
## [16] "NR4A2"      "TCP11L2"    "TGIF1"      "ZFAS1"      "ZFP36L1"   
## [21] "LTBP4"      "PRR14L"     "SETD5"      "ZBTB40"    
## [1] "found 21 genes."

## [1] 36
##  [1] "C10orf91"    "AC020659.1"  "ANKRD36B"    "ANKRD36C"    "BICRAL"     
##  [6] "CHD9"        "COL6A2"      "COL6A3"      "CPPED1"      "DENND4B"    
## [11] "EHBP1L1"     "IQCG"        "LAIR2"       "MINDY2"      "NLRC3"      
## [16] "RAB27B"      "RNF19A"      "SLC16A1-AS1" "SYTL3"       "TRDC"       
## [21] "TTC16"       "VPS13C"      "VTI1A"       "XCL1"        "ZNF708"     
## [1] "found 22 genes."

## [1] 37
##  [1] "BACH2"    "EGR1"     "FOSB"     "HIST1H4C" "JUNB"     "MAF1"    
##  [7] "NUCB2"    "RGS10"    "RPL22L1"  "SEPT6"    "SNHG8"    "TSR3"    
## [13] "ACAP3"    "ARRDC3"   "CYTH1"    "FOSL2"    "JUND"     "L3HYPDH" 
## [19] "MAF"      "MIDN"     "POLR3D"  
## [1] "found 20 genes."

## [1] 38
##  [1] "CD83"     "COG5"     "HMBOX1"   "IKZF2"    "KIF9"     "NXT2"    
##  [7] "ANKRD36"  "ANKRD49"  "BCL9L"    "CD226"    "COG7"     "FNBP1"   
## [13] "INPP4A"   "IRAK4"    "PPP1R16B" "RAP1GAP2" "SPN"      "SSBP3"   
## [19] "THADA"    "UVRAG"    "VPS18"    "VPS39"    "XPO6"    
## [1] "found 23 genes."

## [1] 39
##  [1] "AL136454.1" "SERINC5"    "ABCA5"      "ADHFE1"     "CHD6"      
##  [6] "DDIT4"      "DDX3Y"      "DUS1L"      "EIF1AY"     "ENOSF1"    
## [11] "FGL2"       "GBP5"       "HECTD4"     "ISG20"      "KDM5D"     
## [16] "KIAA1109"   "LPIN1"      "OSM"        "PARP11"     "RPS4Y1"    
## [21] "SBNO2"      "SUSD6"      "TARSL2"     "ZMIZ2"      "ZNF236"    
## [1] "found 23 genes."

## [1] 40
##  [1] "CXorf57" "ID1"     "PLK2"    "SBF2"    "ABR"     "ANKRD44" "EHD4"   
##  [8] "EIF4E3"  "FAM53B"  "H6PD"    "MYOM2"   "NEK9"    "NRDE2"   "PPIL2"  
## [15] "PRDM2"   "PTGDS"   "RBSN"    "RREB1"   "SBF1"    "TBC1D2B" "TMX3"   
## [22] "UQCC2"   "ZNF407"  "ZNF827" 
## [1] "found 24 genes."

Session information

gc()
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  4190026 223.8   11673970 623.5         NA 11673970 623.5
## Vcells 20600971 157.2   61723001 471.0      65536 61693859 470.7
sessionInfo()
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] stringr_1.5.0     limma_3.54.2      tidyr_1.3.0       ggpubr_0.6.0     
## [5] ggplot2_3.4.2     data.table_1.14.8
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.10            png_0.1-8              Biostrings_2.66.0     
##  [4] digest_0.6.31          utf8_1.2.3             R6_2.5.1              
##  [7] GenomeInfoDb_1.34.9    backports_1.4.1        stats4_4.2.3          
## [10] RSQLite_2.3.1          evaluate_0.20          httr_1.4.6            
## [13] pillar_1.9.0           zlibbioc_1.44.0        rlang_1.1.0           
## [16] rstudioapi_0.14        car_3.1-2              jquerylib_0.1.4       
## [19] blob_1.2.4             R.oo_1.25.0            R.utils_2.12.2        
## [22] S4Vectors_0.36.2       rmarkdown_2.21         labeling_0.4.2        
## [25] RCurl_1.98-1.12        bit_4.0.5              munsell_0.5.0         
## [28] broom_1.0.4            compiler_4.2.3         xfun_0.39             
## [31] pkgconfig_2.0.3        BiocGenerics_0.44.0    htmltools_0.5.5       
## [34] tidyselect_1.2.0       KEGGREST_1.38.0        GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1           IRanges_2.32.0         fansi_1.0.4           
## [40] crayon_1.5.2           dplyr_1.1.2            withr_2.5.0           
## [43] R.methodsS3_1.8.2      bitops_1.0-7           grid_4.2.3            
## [46] jsonlite_1.8.4         gtable_0.3.3           lifecycle_1.0.3       
## [49] DBI_1.1.3              magrittr_2.0.3         scales_1.2.1          
## [52] cli_3.6.1              stringi_1.7.12         cachem_1.0.7          
## [55] carData_3.0-5          farver_2.1.1           XVector_0.38.0        
## [58] ggsignif_0.6.4         bslib_0.4.2            generics_0.1.3        
## [61] vctrs_0.6.2            RColorBrewer_1.1-3     org.Hs.eg.db_3.16.0   
## [64] tools_4.2.3            bit64_4.0.5            Biobase_2.58.0        
## [67] glue_1.6.2             purrr_1.0.1            abind_1.4-5           
## [70] fastmap_1.1.1          yaml_2.3.7             AnnotationDbi_1.60.2  
## [73] colorspace_2.1-0       rstatix_0.7.2          memoise_2.0.1         
## [76] knitr_1.44             sass_0.4.5